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Related Concept Videos

Chromatin Packaging01:32

Chromatin Packaging

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a...
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The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a...
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Nucleosome Remodeling02:54

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Smooth DNA transport through a narrowed pore geometry.

Spencer Carson1, James Wilson2, Aleksei Aksimentiev2

  • 1Department of Physics, Northeastern University, Boston, Massachusetts.

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DNA translocation through nanopores becomes regular when pore diameter limits DNA self-interaction. This finding enables precise DNA mapping and sizing, advancing genomics and biotechnology applications.

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Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Biophysics

Background:

  • Voltage-driven DNA translocation through nanopores is crucial for biotechnology but poorly understood at the microscopic level.
  • Previous studies noted pore size-dependent transport kinetics, with sub-5 nm pores showing heterogeneous DNA dwell times.

Purpose of the Study:

  • To investigate the role of DNA self-interaction in anomalous transport through nanoscale pores.
  • To identify conditions for regular DNA translocation and characterize its scaling behavior with DNA length.

Main Methods:

  • Utilized a nanopore device to study voltage-driven double-stranded DNA translocation.
  • Analyzed DNA dwell time distributions and their dependence on pore diameter and DNA length (35-20,000 bp).
  • Assessed the device's resolution by discriminating DNA fragments of different sizes.

Main Results:

  • Anomalous DNA transport in sub-5 nm pores is attributed to pore-diameter-dependent DNA self-interaction.
  • Identified a regime of regular DNA transport with narrow dwell-time distributions fitting drift-diffusion theory.
  • Observed a single power-law scaling of 1.37 for dwell time versus DNA length.
  • Achieved >98% accuracy in discriminating 100 and 500 bp DNA fragments.

Conclusions:

  • Controlling DNA self-interaction via pore diameter is key to achieving regular translocation.
  • The observed power-law scaling and high discrimination accuracy support applications in DNA mapping and sizing.
  • Smooth DNA translocation facilitates advancements in genomics and quantitative molecular biology.